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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Related Experiment Video

Updated: May 26, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Performance of genotype imputations using data from the 1000 Genomes Project.

Yun Ju Sung1, Lihua Wang, Tuomo Rankinen

  • 1Division of Biostatistics, School of Medicine, Washington University in St. Louis, Mo. 63110, USA. yunju@wubios.wustl.edu

Human Heredity
|January 4, 2012
PubMed
Summary

Genotype imputation using 1000 Genomes (1KG) data significantly increases the number of imputed SNPs compared to HapMap data, offering greater potential for discovering associations with rare variants.

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Infinium Assay for Large-scale SNP Genotyping Applications
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

  • Genetics
  • Bioinformatics
  • Genomic Data Analysis

Background:

  • Genotype imputation is crucial for genome-wide association studies (GWAS).
  • 1000 Genomes (1KG) Project data offers a larger reference panel than HapMap data.
  • Limited evaluations exist for 1KG-based genotype imputation performance.

Purpose of the Study:

  • To empirically evaluate genotype imputation performance using 1KG reference panels.
  • To compare 1KG imputation performance against widely used HapMap Phase II data.
  • To assess the impact of 1KG data on imputing rare and low-frequency variants.

Main Methods:

  • Utilized three reference panels: CEU (HapMap II & 1KG) and EUR (1KG).
  • Genotyped 324,607 autosomal SNPs in 501 European ancestry individuals.
  • Compared imputation yield and accuracy against HapMap Phase II data.

Main Results:

  • 1KG reference panels yielded over twice the number of imputed SNPs (6.7 million vs. 2.5 million) compared to HapMap II.
  • Imputation accuracy with 1KG panels was high and comparable to HapMap II.
  • Accuracy for rare, low-frequency, and common SNPs was very high after filtering.

Conclusions:

  • 1KG-based imputation substantially increases imputation yield and maintains high accuracy.
  • The 1KG-EUR panel showed advantages in imputing variants across the allele frequency spectrum.
  • 1KG-based imputation enhances the discovery of significant associations for SNPs, with potential for future improvements.